Hydropathy profile

Figure 3. Hydropathy Profile and mature protein primary sequence of the deduced p-Subunit Precursor Protein.

Upper panel The hydropathy profile of the entire 69 kD precursor protein is shown. The abscissa is amino acid residues and the ordinate, positive values indicate hydrophilic. The black and hatched rectangles at the bottom of the figure denote the calculated signal sequence and amino-terminal propeptide domains, respectively. The mature and carboxyl-terminal domains are labeled. N-linked core glycosylation consensus sites are depicted by branched structures. 

The cellulose 4-p-glucosyltransferase of Acetobacter xylinum exhibits 42.8 % identity at the DNA level and 26.2 % identity at the whole deduced amino add level to the pcs A2 polypeptide. The cotton cel Al polypeptide exhibits 53.9 % identity at the DNA level and 68.7 % identity at the amino add level to the pcs A2 polypeptide. The hydropathy profiles suggest at least two transmembrane helices, e.g., one is located in the N-terminal region and one is in C-terminal region. The central regions of the polypeptides are rather hydrophilic and are... 

Structural similarities can be seen, however, when the hydropathy profiles of the tobacco and Arabidopsis ALS transit peptides are compared (not shown). This suggests that a functional transit sequence depends more on secondary or higher order structural constraints than on primary sequence information. The in vitro uptake system described above can be used to further investigate the transit peptide domain. 

Figure 16-15 shows the hydropathy profiles for three different membrane proteins. The prominent peaks in such plots Identify probable topogenic sequences, as well as their position and approximate length. For example, the hydropathy profile of the human growth hormone receptor reveals the presence of both a hydrophobic signal sequence at the extreme N-termlnus of the protein and an internal hydrophobic stop-transfer sequence (see Figure 16-15a). On the basis...

The topology of membrane proteins can often be correctly predicted by computer programs that identify hydrophobic topogenlc segments within the amino acid sequence and generate hydropathy profiles (see Figure 16-15). 

M. Degli Esposti, M. Crimi, and G. Venturoli, A critical evaluation of the hydropathy profile of membrane proteins, Eur. J. Biochem. 190, 207-219 (1990). 

The PSI-I subunit is very hydrophobic (polarity index 0.28) and tightly bound to CPI at conditions otherwise used to dissociate the low molecular mass polypeptides from CPI. The hydropathy profile of the PSI-I polypeptide indicates the presence of a central hydrophobic region flanked by hydrophilic N- and C-terminals. The hydrophobic region is predicted to form an a-helix which may span the thylakoid membrane. 

Apart from these well-known desaturases we have found several sequences with three complete histidine boxes and the characteristic hydropathy profiles, which cannot be assigned to any of the branches identified so far. Therefore, this group (7-9) represents a separate branch to be identified yet by functional expression. The last group included in the dendrogram comprises acyl-CoA desaturases (1-6). They represent a clearly separated family, which in itself is deeply bifurcated. 

Fig. 3. Hydropathy profile of the sequence of the M-subunit using a moving window of 19 amino acids. Positions of basic (Lys, Ag) and acid (Glu, Asp) are denoted by and Q. Solid line indicates residues obtained by peptide analysis (from Ref. 8).

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